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From how i see it, the MK II was really only out matched by the transforming MS's because of the obvious. They tended to have more fire power and were faster.
But a point I'd like to bring up is machine vs machine, anything with a beam weapon could take it out. Hell with its reduced armor OYW Zeon suits may have a better chance at killing it then the first set of gundams.
Same goes with the Zeta, machine vs machine a single beam shot will take it out. And again with its reduced armor and the suposive less durable frame i keep reading about, conventional slug weapons may be more effective on it. BUT it has the nifty transforming gimmic.
Now you start talking about pilots then things start to get vague and shit storms start forming. Because now your not talking about the machine, your talking about a pilot's skill and their "plot armor".
Some one asked if the Alex or the GPO types could take on the Mk II. Yes they can, machine on machine again a beam rifle strike is going to wreak the Mk II, just like it would wreak them. The Alex's hidden 90mm guns are likely effective as well because again the Mk II doesn't have the armor the first set of gundams have.